I think that pindel is fine. The issue may relate to the general issues of calling indels from NGS data.
Some things to consider:
- Have you visually look at how the reads have aligned over the regions
in which indels were not called? They may be problematic regions,
like for example homopolymeric regions. I would load your aligned
BAMs into IGV
- Check your mapping quality (MAPQ) filter thresholds (reads with
indels will automatically receive lo MAPQ unless we specifically
treat them differently
- Consider your indel length in relation to your read length. As you're
using Ion Torrent, I guess that your reads are ~75bp? If you are
trying to detect indels from reads of this size, it will always be
difficult.
- Consider downloading your BAMs from the Torrent Server and then using
something like GATK IndelRealigner followed by HaplotypeCaller in
order to attempt to identify the indels.
